Microbiome Data Visualization

Do you know how to read .qza file?

## Reading and exploring Artifacts (.qza)
SVs <- read_qza(file = "data/feature_table.qza", tmp = "data/tmpdir", rm = TRUE)

SVs$data[1:4,1:4]

otu_table(q2_ps)[1:4,1:4]

## Reading metadata
read_q2metadata("data/sample_metadata.tsv")[1:5, 1:5]

read_tsv("data/sample_metadata.tsv", comment = "#q2:types", show_col_types = FALSE)[1:5, 1:5] %>% 
  rename(SampleID="#SampleID")

## Reading taxonomy
taxonomy<-read_qza("data/taxonomy.qza")
head(taxonomy$data)

## Parse tidy taxonomy only
taxonomy<-parse_taxonomy(taxonomy$data)
head(taxonomy)


Citation

Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.


References

[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4


Appendix

Project main tree

.
├── LICENSE
├── README.md
├── Rplots.pdf
├── config
│   ├── config.yml
│   ├── pbs
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   ├── samples.tsv
│   ├── slurm
│   │   ├── cluster.yaml
│   │   └── config.yaml
│   └── units.tsv
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature_table.qza
│   ├── features.csv
│   ├── metadata.csv
│   ├── metadata.tsv
│   ├── q2_demo_ps.rds
│   ├── q2_ps.rds
│   ├── sample_metadata.tsv
│   ├── shannon.csv
│   ├── shannon.qza
│   ├── taxonomy.csv
│   └── taxonomy.qza
├── figures
│   ├── heatmap.png
│   ├── heatmap.svg
│   ├── jitterplot.png
│   ├── jitterplot.svg
│   ├── lineplot.png
│   ├── lineplot.svg
│   ├── pcoa.png
│   ├── pcoa.svg
│   ├── venndiagram.png
│   └── venndiagram.svg
├── images
│   ├── bkgd.png
│   ├── coders.png
│   ├── ml.png
│   ├── smkreport
│   │   └── screenshot.png
│   └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── export.bib
│   ├── imap.bib
│   └── references.bib
├── report.html
├── resources
│   ├── feature_table.qza
│   ├── rooted_tree.qza
│   ├── sample_metadata.tsv
│   ├── shannon_vector.qza
│   ├── tax.qza
│   ├── taxonomy.qza
│   └── unweighted_unifrac_pcoa.qza
├── results
│   └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
    ├── Snakefile
    ├── envs
    │   ├── environment.yml
    │   ├── mothur.yml
    │   └── qiime220232.yml
    ├── report
    │   ├── boxplots.rst
    │   ├── hcluster.rst
    │   ├── heatmap.rst
    │   ├── jitterplot.rst
    │   ├── lineplot.rst
    │   ├── nmds.rst
    │   ├── pcaordi.rst
    │   ├── pcoa.rst
    │   ├── scatter.rst
    │   ├── venndiagram.rst
    │   └── workflow.rst
    ├── rules
    │   ├── qiime2_viz.smk
    │   ├── render_index.smk
    │   ├── rmd_report.smk
    │   └── rules_dag.smk
    └── scripts
        ├── README.md
        ├── common.R
        ├── convert_qiime2csv.R
        ├── heatmap.R
        ├── import_qiime2_data.R
        ├── jitterplot.R
        ├── lineplot.R
        ├── pcoa.R
        ├── qiime2R.R
        ├── qiime2_phyloseq_object.R
        ├── render.R
        ├── rules_dag.sh
        ├── smk_html_report.sh
        ├── tree.sh
        └── venndiagram.R

16 directories, 89 files


Unlocking working directory.
Building DAG of jobs...
Creating report...
Adding venndiagram.svg (0.17 MB).
Adding lineplot.svg (0.016 MB).
Adding jitterplot.svg (0.014 MB).
Adding pcoa.svg (0.014 MB).
Adding heatmap.svg (0.19 MB).
Loading script code for rule qiime2_phyloseq_object
Loading script code for rule import_qiime2_data
Loading script code for rule import_demo_qiime2_data
Loading script code for rule venn_diagram
Loading script code for rule convert_qiime2csv
Loading script code for rule line_point_plot
Loading script code for rule jitter_plot
Loading script code for rule pcoa_ordination
Loading script code for rule heatmap_plot
Downloading resources and rendering HTML.
Report created: report.html.
[0409/105921.934209:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0409/105921.937937:ERROR:file_io.cc(91)] ReadExactly: expected 8, observed 0
[0409/105921.941715:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0409/105923.039283:ERROR:command_buffer_proxy_impl.cc(125)] ContextResult::kTransientFailure: Failed to send GpuControl.CreateCommandBuffer.
[0409/105926.727514:INFO:headless_shell.cc(653)] Written to file /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png.
Created 1 file(s):
    /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png


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